SEQUENCE ALIGNMENT IN MOLECULAR-BIOLOGY

Molecular biology is becoming a computationally intense realm of conte mporary science and faces some of the current grand scientific challen ges. In its context, tools that identify, store, compare and analyze e ffectively large and growing numbers of bio-sequences are found of inc reasingly crucial importance. Biosequences are routinely compared or a ligned, in a variety of ways, to infer common ancestry, to detect func tional equivalence, or simply while searching for similar entries in a database. A considerable body of knowledge has accumulated on sequenc e alignment during the past few decades. Without pretending to be exha ustive, this paper attempts a survey of some criteria of wide use in s equence alignment and comparison problems, and of the corresponding so lutions. The paper is based on presentations and literature given at t he Workshop on Sequence Alignment held at Princeton, N,J,, in November 1994, as part of the DIMACS Special Year on Mathematical Support for Molecular Biology.